Spliceosomal trans-splicing generally involves the intermolecular ligation of RNA sequences derived from two independent RNA molecules. A form of trans-splicing is spliced leader (SL) trans-splicing in which a short RNA leader sequence, the spliced leader (approximately 15-50 nt), is transferred from the 5′ end of a specialized non-messenger RNA molecule (SL donor RNA) onto unpaired splice-acceptor sites on pre-mRNA molecules to become the 5′-end of the mature mRNA. As a result, diverse mRNAs acquire a common 5′ leader sequence.
SL RNAs, the RNAs that contribute or “donate” the spliced leader to another RNA transcript, are short RNAs (approximately 45-140 nt) that contain a splice-donor site but no splice-acceptor site. Although SL RNAs have little primary sequence conservation across phyla, various SL RNA sequences share a conserved, three-stem-loop secondary structure (see, for review, Mayer and Floeter-Winter, Mem. Inst. Oswaldo Cruz 100:501-13, 2005). They have an overall structural similarity to Sm-class U-rich small nuclear RNAs (snRNAs) which are present in spliceosomal small ribonucleoprotein complexes (snRPNs) and participate in the splicing mechanism. The splice-donor site functionally divides the SL RNA molecule into two segments. During splicing, the 5′-segment (i.e. the leader sequence) behaves like the first exon in a conventionally-expressed gene, and the 3′-segment behaves like the 5′-part of a conventional intron that gets “spliced out” when the splicing product is generated. SL RNAs are associated with spliceosomal (Sm) proteins and specific non-Sm proteins that interact in vivo with other splicing components in snRPNs.
SL trans-splicing has been considered as a general mechanism that may be required for the production of mature transcripts in some species. It has been further documented that in some cases spliced leaders also play a role in enhancing gene expression. Their proposed functions in this regard include (i) increasing the stability of trans-spliced transcripts, (ii) enabling or enhancing the transport of mature transcripts out of the nucleus to the cytoplasm where they are subsequently translated, and (iii) facilitating the assembly of complete ribosome with large and small subunits at the AUG initiation codon, thereby allowing efficient translation. Other roles for SLs in various species include: providing a 5′-cap structure for protein-coding RNAs transcribed by the rRNA polymerase, Pol I; generating mature monocistronic mRNAs from polycistronic pre-mRNA transcripts; and other roles, as reviewed previously (Hastings et al., Trends in Genetics 21:240-47, 2005). In some instances, SL trans-splicing can turn polycistronic transcripts into translatable, monocistronic mRNAs by transplanting a short (about 15-50 nucleotide) fragment from a donor RNA—the SL sequence—onto the 5′ ends of separate pre-mRNAs transcribed as one, long polycistron. Each pre-mRNA in the polycistron has an intron that contains a spliceosomal (Sm) binding site believed to facilitate splicing.
SL trans-splicing has been studied extensively in Euglenozoa and has been detected in a limited but diverse number of eukaryotes including appendicularia, ascidians, cnidarians, nematodes, Platyhelminthes, and rotifers. More recently, SL RNA trans-splicing with a unique and conserved spliced leader sequence (22-nt) has been reported in a number of dinoflagellates (Zhang et al. Proc. Natl. Acad. Sci. USA 104:4618-4623, 2007).